Software Map

Genpak is a small set of utilities designated to process DNA, RNA, and protein sequences in a very Un*x-like manner. This way, Genpak programs can be combined using pipes and redirections, as well as easily incorporated into CGI scripts. The utilities include a program for calculating GC content, Tm, translating DNA/RNA sequences into protein sequences, quick sequence retrieval, random sequence generation, and finding promoter sequences using a Hertz matrix.

EGO is a program to perform molecular dynamics simulations on parallel as well as on sequential computers. Supported parallel machines include the Hitachi SR8000, CRAY-T3E, IBM-SP2, Fujitsu VPP700, Parsytec-CC under PARIX, and inhomogeneous clusters of UNIX workstations under PVM or MPI. EGO also runs sequentially on any decent UNIX workstation, even Windows95/NT PC's (with a GNU-C compiler) can be used.

slcview allows you to fully script creation of
clustergrams and tree diagrams from .cdt, .gtr,
and .atr files as output by several
biologically-oriented clustering programs, namely
Cluster and XCluster. Many options allow you
control of the output, and, in addition, slcview
allows you to create an annotated legend with the
same scale of colors as used in your clustergram.

Adun is an extensible biomolecular simulation
program that includes data
management and analysis capabilities.

The Digital Seed Vault is a seed stock database mainly developed for researchers in the plant sciences. It can also be used by people who handle a lot of different seeds, e.g. garden enthusiasts, seed breeders, or seed producers.

SIGHT is a code generator set to create a user-defined system of Web robots, realising arbitrary workflow. It generates Web robots that can be based on Stalker algorithm, HTML structure, etc. This task is frequent in bioinformatics.

Yawn (Yet Another {Weird | Wacky | Witty |
Wonderful | W*} Network) is a Java framework for
training and testing neural networks independently
from the neural model and the test environment
being used. The models implemented so far are
AppART, GasART, fuzzy ARTMAP, and Multi-Layer
Perceptron (MLP).

ProteomeCommons.org IO Framework is a proper Java
framework for handling spectra and peak lists. The
framework can read and write to a number of
different spectra and peak list formats, and it
provides a simple, intuitive Java object model for
working with spectra or peak lists. All classes
support two methods of handling peak list and
spectrum data: in-memory or stream. The goal of
this framework is to support all the popular MS
and MSMS data formats, and to eliminate any time
or effort involved in figuring out how to read and
write peak list or spectrum files.

QtIPy is a simple GUI-based automator for IPython notebooks. It allows you to attach triggers to files, folders, or timers to automatically run notebooks. IPython notebooks are great for interactively working through analysis problems, so why would you want to automatically run them? To get a record of how you ran your analysis! By running a notebook through QtIPy you get the output, figures, and a step by step log of how the analysis was performed all in the same folder.

Quick-Join implements a heuristic for speeding up
neighbour joining, making neighbour joining feasible for
large sets of taxa. The inferred tree is identical to the
tree inferred by the traditional neighbour joining
method, but the heuristic will (potentially) construct the
tree significantly faster.

StrBio is a set of Java classes useful for development of software for
computational structural biology research.

Analyze ECGs is a graphical data analysis tool for use on
analog input DAQ data, such as that of RTLab. It is
useful for opening the '.nds' file format produced by
RTLab's data acquisition program, DAQSystem (it can
also open regular ASCII files). Aside from being a
general-purpose multichannel analog data editing tool, it
also contains custom features useful for analyzing cardiac
data. However, it can be used for editing/viewing
general-purpose data as well. Additionally, this program
can convert '.nds' files to ASCII format data.

Fingerprint-POC is a fingerprint matching
application using the Phase-Only Corelation method.

OmniGene is a bioinformatics solution with a user
interface inspired by Ensembl, middleware capable
of connecting to disparate datasources, and a
translation facility for common biological file
formats.